ClinVar Miner

Submissions for variant NM_001085487.3(MYSM1):c.219-1G>A

gnomAD frequency: 0.00016  dbSNP: rs201886018
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002029309 SCV002305504 likely pathogenic not provided 2025-01-22 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 3 of the MYSM1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in MYSM1 are known to be pathogenic (PMID: 24288411, 28115216). This variant is present in population databases (rs201886018, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with MYSM1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1514455). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV003120803 SCV003799016 likely pathogenic Bone marrow failure syndrome 4 2022-12-08 criteria provided, single submitter clinical testing PP3_Strong, PM2
PreventionGenetics, part of Exact Sciences RCV003418340 SCV004114832 likely pathogenic MYSM1-related disorder 2023-01-30 criteria provided, single submitter clinical testing The MYSM1 c.219-1G>A variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.023% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-59156090-C-T). Variants that disrupt the consensus splice acceptor site in MYSM1 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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